Search found 32 matches

by jklinck
Thu Mar 28, 2019 1:22 pm
Forum: ROMS Discussion
Topic: Baroclinic instability demonstration
Replies: 0
Views: 352

Baroclinic instability demonstration

I am using ROMS as part of a GFD class as a way to demonstrate some processes that are hard to show with analytical math. My latest failure is to illustrate baroclinic instability using a periodic zonal channel with linearly stratified (both y and z) initial conditions (matching the setup in G Valli...
by jklinck
Thu May 10, 2018 2:48 pm
Forum: ROMS Bugs
Topic: all result = 0?
Replies: 22
Views: 3406

Re: all result = 0?

To add to Kate's suggestion, I would run this model for about 10 time steps having compiled with debug on in the compile script (however you compile the model). Run in scalar mode (one processor). Make sure that you turn on array bounds checking. This makes sure that arrays are defined and indexes a...
by jklinck
Mon May 07, 2018 1:14 pm
Forum: ROMS Bugs
Topic: all result = 0?
Replies: 22
Views: 3406

Re: all result = 0?

Given the values in the wind forcing file (10^34), I think these are all "missing values" for netcdf. Are you sure that you assigned variables to the forcing file? I would plot the wind speeds in the forcing file to see that they are what you wanted. If the forcing file is ok, then make sure that th...
by jklinck
Mon Jul 24, 2017 9:25 pm
Forum: ROMS Bugs
Topic: Difference between trunk/ROMS and COAWST/ROMS with Qout
Replies: 3
Views: 2062

Re: Difference between trunk/ROMS and COAWST/ROMS with Qout

John, My thanks to Ivicia. Adding the 4 lines fixed the problem. I can run the upwelling case and the estuary test without sediments. Thanks for the quick response. I am trying to set up an all analytical test ACC/Atlantic overturning model with sea ice (and maybe ice shelves). I will send you the s...
by jklinck
Mon Jul 24, 2017 4:31 pm
Forum: ROMS Bugs
Topic: Difference between trunk/ROMS and COAWST/ROMS with Qout
Replies: 3
Views: 2062

Difference between trunk/ROMS and COAWST/ROMS with Qout

There is a curious difference between COAWST/ROMS(v1175) and trunk/ROMS (v854). The source code for both were obtained last week (July 20 2017). The problem: I am trying to run the upwelling case in COAWST/ROMS to set up the environment. Both scalar and mpi compiles report an incorrect model configu...
by jklinck
Tue Jan 24, 2017 2:30 pm
Forum: ROMS Ecosystem
Topic: Correction to fennel.h
Replies: 2
Views: 1581

Re: Correction to fennel.h

I think this is an error that I created (sorry to add confusion). I started with the spect_fennel.h model (svn 2232 2012-01-03) in the COAWST distribution (svn 1000, distributed Dec 15, 2014). I changed the spectral light representation in hte code based on GRASSLIGHT (a shallow water optical/vegita...
by jklinck
Mon Jan 23, 2017 7:49 pm
Forum: ROMS Ecosystem
Topic: Correction to fennel.h
Replies: 2
Views: 1581

Correction to fennel.h

This error may have been identified before, but I did not see anything in the ecosystem discussion. Depending on how folks develop other ecosystem models, this error might have migrated to other ecosystem codes. At the end of the sinking code in fennel.h, there are statements to remineralize phytopl...
by jklinck
Fri Dec 16, 2016 5:21 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 6468

Re: Climatology and nudging in ecosystem models

I have figured out how nudging to climatology works, by doing some experiments. Here is my understanding, but I am happy to hear another explanation. The climatology arrays are created (and indexed) in the order in which climatology is processed. In my case, I have 16 tracers (T,S, 4 sediment and 10...
by jklinck
Thu Dec 15, 2016 8:40 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 6468

Re: Climatology and nudging in ecosystem models

The bio input file has the following lines:

LtracerCLM = 12*T
LnudgeTCLM = 12*T

so climatology should be managed and used.

Nudging to climatology does work with the imposed indexes, but the wrong variables are nudged to the wrong values.

John
by jklinck
Thu Dec 15, 2016 8:31 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 6468

Re: Climatology and nudging in ecosystem models

My "clever" solution to use explicit indexes for the climatology does not work. The climatology arrays don't have the indexes that I expect so the nudging is wrong. I have gone back to the "proper" way to have a climatology. I could not find any example of a biological model that uses a climatology,...
by jklinck
Wed Dec 14, 2016 10:01 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 6468

Climatology and nudging in ecosystem models

I have an ecosystem model (a modification from Fennel.h) in which I would like to nudge nutrients to climatology. I am trying to define the climatology in ana_tclima.h with statements like those below. I also include "use mod_biology" in the module section which should give access to the biological ...
by jklinck
Fri Feb 19, 2016 2:27 pm
Forum: ROMS Usage
Topic: alternating flow in constant depth channel.
Replies: 1
Views: 1616

alternating flow in constant depth channel.

I am trying to set up roms to represent alternating flow in a uniform depth channel (x-z). It is 40 km long and periodic in y. density is uniform. vertical viscosity is constant. The boundaries are open on east and west ends. I want the flow to have ubar = uo sin(2 pi t/period) for different choices...
by jklinck
Wed Dec 09, 2015 1:19 pm
Forum: ROMS Problems
Topic: Checkerboard instability
Replies: 7
Views: 3451

Re: Checkerboard instability

A checkerboard instability pattern is due horizontal diffusion/viscosity. Look at your time step relative to the grid spacing and horizontal diffusivity. With laplacian horizontal diffusivity A dt / dx^2 needs to be less than 1 (maybe 1/2) depending on the time stepping scheme. With variable horizon...
by jklinck
Thu Oct 15, 2015 5:02 pm
Forum: ROMS Usage
Topic: surface mass sources (but not rivers)
Replies: 3
Views: 1496

Re: surface mass sources (but not rivers)

I was able to set up the source/sink flow based on John's suggestion (Thanks!). I can get a linear abyssal circulation driven by surface sources and sinks using LwSrc=true and LuvSrc=false, and using ana_psource.h to control sources/sinks. The model limits the number of sources to 200. I have a 100x...
by jklinck
Thu Oct 08, 2015 7:04 pm
Forum: ROMS Usage
Topic: surface mass sources (but not rivers)
Replies: 3
Views: 1496

surface mass sources (but not rivers)

I would like to use roms to demonstrate the abyssal circulation in a homogeneous density model by applying surface mass sources and sinks. Is there a way to add mass to change d zeta/dt? ana_psource seems to be designed as a lateral mass source (rivers) which also adds momentum along with mass. I am...
by jklinck
Mon Aug 03, 2015 4:54 pm
Forum: Job Opportunities
Topic: Asst Professor position Old Dominion Univ in coastal process
Replies: 0
Views: 3265

Asst Professor position Old Dominion Univ in coastal process

The Department of Ocean, Earth and Atmospheric Sciences at Old Dominion University invites applications for a tenure-track faculty position to begin by fall 2016 in the area of coastal systems and processes. Specific areas of research we are most interested include: • Processes and histories of sedi...
by jklinck
Fri Feb 13, 2015 7:16 pm
Forum: ROMS Ecosystem
Topic: light units for ec_Fobar
Replies: 1
Views: 1693

light units for ec_Fobar

What are the units for the light values (ec_Fobar) in mod_eclight? I am trying to compare this model to the one in Gregg and Carder (1990) where Ho in that paper has units of W/m2/nanometer. These value differ by about 10. Are these values in micromole photons/m2/s? Converting these units don't give...
by jklinck
Thu Oct 31, 2013 5:12 pm
Forum: Job Opportunities
Topic: Assistant Professor opening at ODU
Replies: 0
Views: 2071

Assistant Professor opening at ODU

Tenure Track Faculty Position in Physical Oceanography The Department of Ocean, Earth and Atmospheric Sciences at Old Dominion University (http://sci.odu.edu/oceanography/) invites applications for a tenure track position as Assistant or Associate Professor in Physical Oceanography. We seek a broad-...
by jklinck
Mon Jan 07, 2013 6:27 pm
Forum: Job Opportunities
Topic: Faculty position in Physical Oceanography at Old Dominion U
Replies: 0
Views: 2570

Faculty position in Physical Oceanography at Old Dominion U

Tenure Track Faculty Position in Physical Oceanography[/b] The Department of Ocean, Earth and Atmospheric Sciences at Old Dominion University (http://sci.odu.edu/oceanography/) invites applications for a tenure track position as Assistant or Associate Professor in Physical Oceanography. Preference w...
by jklinck
Wed Aug 29, 2012 4:49 pm
Forum: Job Opportunities
Topic: Postdoc opportunity at ODU - Antarctic regional models
Replies: 0
Views: 1978

Postdoc opportunity at ODU - Antarctic regional models

POST-DOCTORAL RESEARCH ASSOCIATE - #12035 Post-doctoral Research Associate in Physical Oceanography. The Center for Coastal Physical Oceanography, Old Dominion University has four ongoing NSF-funded projects (Co-PIs: J. Klinck, M. Dinniman and E. Hofmann) focused on various aspects of interactions b...
by jklinck
Mon Jul 11, 2011 12:22 pm
Forum: ROMS Discussion
Topic: ROMS Particle Tracking
Replies: 5
Views: 3273

Re: ROMS Particle Tracking

The 4th order milne scheme was tested for accuracy against analytical flow (purely circular flow with oscillating vertical migration). The largest cause for error was the interpolation from the grid points to the particle location. With analytical flow fields (no interpolation) the path error was le...
by jklinck
Wed Aug 25, 2010 11:58 am
Forum: ROMS Tools and Techniques
Topic: question about plotting
Replies: 5
Views: 3103

Re: question about plotting

I have seen this problem with the use of IDT, which is an interactive translator for ncar metacode. I have had trouble installing ncar graphics and getting idt to work. Try the following test ctrans -d X11 gmeta which is the non-interactive metacode translator. This should open a window and show the...
by jklinck
Thu Jun 24, 2010 1:32 pm
Forum: ROMS Discussion
Topic: second order ODE in ROMS
Replies: 4
Views: 926

Re: second order ODE in ROMS

The requirement of a very short time step must be due to a fast rate in your equations. First order schemes (like Euler) are almost always poor performers. That is, they give bad solutions but are not unstable for a short enough time step. Any of the schemes you mention should behave. The ~1 sec tim...
by jklinck
Tue Jun 22, 2010 1:15 pm
Forum: ROMS Discussion
Topic: second order ODE in ROMS
Replies: 4
Views: 926

Re: second order ODE in ROMS

The problem you are having is not clear from your message. Any 2nd order ode can be set up as two coupled 1st order ode. Have you tried solving the ODE with a different solver independent of ROMS? How small must the time step be to get a stable solution? If all else fails, code your own 2nd order Ru...
by jklinck
Thu Oct 15, 2009 3:37 pm
Forum: Job Opportunities
Topic: Postdoc Opportunity at ODU. Antarctic Coastal Modeling
Replies: 0
Views: 1312

Postdoc Opportunity at ODU. Antarctic Coastal Modeling

Research Scientist in Oceanography. Full-time position: to participate in a National Science Foundation-funded project that is focused on understanding the physical mechanisms controlling cross-shelf exchange on Antarctic continental shelves and how this exchange relates to melting of the base of th...
by jklinck
Thu Nov 13, 2008 4:13 pm
Forum: ROMS Discussion
Topic: integration of vertical speed for floats; types of floats?
Replies: 5
Views: 3184

Re: integration of vertical speed for floats; types of floats?

It looks like the vertical calculation is predictor-corrector unless the random walk is on.

I got lost in the cpp statements.

It should be possible to do the random walk with predictor-corrector. I will think about it, but it will be down my list of things to think about.

Thanks,

John
by jklinck
Tue Nov 11, 2008 10:19 pm
Forum: ROMS Discussion
Topic: integration of vertical speed for floats; types of floats?
Replies: 5
Views: 3184

integration of vertical speed for floats; types of floats?

I have noticed in the step_floats routine, that an Euler forward time scheme is used to calculate the vertical position of the float while the horizontal position uses a predictor-corrector scheme. Is there any reason to do this? Has anyone tried the p-c scheme for the vertical equation? As a second...
by jklinck
Thu May 08, 2008 5:48 pm
Forum: ROMS Installation
Topic: Using OPENMP on Sun AMD (intel) for solaris 10
Replies: 3
Views: 1435

I changed the tiling to by 1x2 and ran with 2 threads. (I have another longrunning job and don't want to interfere).

I get the same result-- abnormal termination during the first step.

John
by jklinck
Thu May 08, 2008 5:17 pm
Forum: ROMS Installation
Topic: Using OPENMP on Sun AMD (intel) for solaris 10
Replies: 3
Views: 1435

Using OPENMP on Sun AMD (intel) for solaris 10

I am attempting to run the Upwelling test case on a Sun computer with 2 dual core opteron (AMD) chips with openmp. The calculation blows up in the first long step. Has anyone run ROMS with openmp on SUN opteron using the SunStudio 12 compilers? The OS is solaris 10. Thanks in advance for your help. ...
by jklinck
Thu Aug 30, 2007 11:59 am
Forum: ROMS Ice
Topic: SeaIce issues
Replies: 1
Views: 2465

1D ice models act in unexpected ways. 1) It is very hard to melt ice with solar radiation, especially with a snow layer. Most ice melts by shortwave heating the water and the water melting the ice. Limit your ice concentration to 90 or 95% and you will see faster melt in spring. 2) We had a problem ...
by jklinck
Mon Nov 28, 2005 1:57 pm
Forum: ROMS Problems
Topic: ROMS for highly stratified fuild
Replies: 12
Views: 7972

stratified problem

A baroclinic speed of 3 m/s seems pretty small for strong stratification. Using 320 m depth and a reduced gravity of 2.5 gives an internal wave speed of 28.3 m/s. With a grid spacing of 500 m, I get an internal time step of about 4 sec (making the courant number =1/4, which may not be small enough)....
by jklinck
Fri Dec 05, 2003 8:05 pm
Forum: ROMS Information
Topic: Ice Shelf for ROMS
Replies: 1
Views: 2059

Ice Shelf for ROMS

Hi Hernan and Enrique, I have done more work on the ice shelf startup. The problem with the current setup is that it assumes that the water in which the ice is floating is always rho(zice) , but since the density changes along the base of the ice, this leads to unphysical pressure gradients. Also, t...